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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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Nanopolish with pod5 files #1129

Closed DIPLOMICS-SA closed 2 months ago

DIPLOMICS-SA commented 4 months ago

Hi there, is nanopolish compatible with pod5 files produced by the promethIon?

jts commented 4 months ago

Sorry, nanopolish does not support pod5s. I planned to do this but since there are better options available for most things nanopolish does it wasn't a development priority.

Salvobioinfo commented 4 months ago

Hi @jts Based on your response, can you recommend a tool that can perform a similar function to nanopolish event align, starting from pod5, and produce a similar output (especially when the option --samples is active)?
Thanks in advance.

jts commented 4 months ago

I believe both f5c and uncalled4 can. Or you can use ONT's conversion tools to generate fast5 from pod5.

hasindu2008 commented 4 months ago

Yes. f5c can as long as the POD5 are converted to BLOW5 using bluecrab.

Nanopolish also supports BLOW5, so if you convert to BLOW5 using bluecrab, you can either use nanopolish or f5c.